Details
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Type: Bug
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Status: Open
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Priority: Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Component/s: None
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Labels:None
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Environment:OS X Catalina, most current java
Description
I am trying to obtain consensus sequences from over 100 different alignments using jalview on the command line.
I installed jalview on conda on 9/8/21 and the installation went fine.
Here is my input:
jalview -open GC_00000001_sequences.fa
Here's what I get back:
Running jalview.bin.Jalview with memory setting -Xmx15461881856
Java version: 11.0.9.1
Java Home: /Users/duerkoplab/opt/miniconda3
x86_64 Mac OS X 10.15.7
Jalview Version: 2.11.1.4 (bioconda (build 1) git-commit: [])
# INFO: Setting default net timeout to 30 seconds.
VAqua: installed patch for main/key window support
Exception in thread "main" java.lang.NoClassDefFoundError: sun/awt/image/MultiResolutionImage
at java.base/java.lang.ClassLoader.defineClass1(Native Method)
at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1017)
at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:800)
at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:698)
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:621)
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:579)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:315)
at org.violetlib.aqua.JavaSupport.findImpl(Unknown Source)
at org.violetlib.aqua.JavaSupport.<clinit>(Unknown Source)
at org.violetlib.aqua.AquaLookAndFeel.initialize(Unknown Source)
at java.desktop/javax.swing.UIManager.setLookAndFeel(UIManager.java:586)
at java.desktop/javax.swing.UIManager.setLookAndFeel(UIManager.java:633)
at jalview.bin.Jalview.setSpecificLookAndFeel(Jalview.java:887)
at jalview.bin.Jalview.setVaquaLookAndFeel(Jalview.java:926)
at jalview.bin.Jalview.setMacLookAndFeel(Jalview.java:940)
at jalview.bin.Jalview.setLookAndFeel(Jalview.java:837)
at jalview.bin.Jalview.doMain(Jalview.java:302)
at jalview.bin.Jalview.main(Jalview.java:192)
Caused by: java.lang.ClassNotFoundException: sun.awt.image.MultiResolutionImage
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
... 22 more
I installed jalview on conda on 9/8/21 and the installation went fine.
Here is my input:
jalview -open GC_00000001_sequences.fa
Here's what I get back:
Running jalview.bin.Jalview with memory setting -Xmx15461881856
Java version: 11.0.9.1
Java Home: /Users/duerkoplab/opt/miniconda3
x86_64 Mac OS X 10.15.7
Jalview Version: 2.11.1.4 (bioconda (build 1) git-commit: [])
# INFO: Setting default net timeout to 30 seconds.
VAqua: installed patch for main/key window support
Exception in thread "main" java.lang.NoClassDefFoundError: sun/awt/image/MultiResolutionImage
at java.base/java.lang.ClassLoader.defineClass1(Native Method)
at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1017)
at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:800)
at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:698)
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:621)
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:579)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:315)
at org.violetlib.aqua.JavaSupport.findImpl(Unknown Source)
at org.violetlib.aqua.JavaSupport.<clinit>(Unknown Source)
at org.violetlib.aqua.AquaLookAndFeel.initialize(Unknown Source)
at java.desktop/javax.swing.UIManager.setLookAndFeel(UIManager.java:586)
at java.desktop/javax.swing.UIManager.setLookAndFeel(UIManager.java:633)
at jalview.bin.Jalview.setSpecificLookAndFeel(Jalview.java:887)
at jalview.bin.Jalview.setVaquaLookAndFeel(Jalview.java:926)
at jalview.bin.Jalview.setMacLookAndFeel(Jalview.java:940)
at jalview.bin.Jalview.setLookAndFeel(Jalview.java:837)
at jalview.bin.Jalview.doMain(Jalview.java:302)
at jalview.bin.Jalview.main(Jalview.java:192)
Caused by: java.lang.ClassNotFoundException: sun.awt.image.MultiResolutionImage
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
... 22 more
Attachments
Issue Links
- related with
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JAL-3791 VAqua5-patch.jar does not work (on a mac) with latest AdoptOpenJDK 11 (11.0.9.1+1)
- Closed